Post on 20-Oct-2014
description
23 april 20084th nordic conference on scholarly publishing
lund, sweden
“river blindness”
“river blindness”
“The drug Mectazin has been used effectively, but has to be taken over 15 years and does not kill the adult worm.”
$1,000,000,000
17 years
not only is there no good cure for river blindness...
not only is there no good cure for river blindness...
no one can afford to look.
the knowledge gap
the knowledge gap
we don’t even know how tylenol works.
1.the culture of control
public land
property
socially constructed “property” rights
©
socially constructed “property” rights
©(and patents and trademarks)
socially constructed “property” rights
©“exceptions and limitations”
right of way
constructed rights of waymandatory rights of way
c
GNU logo by Aurelio A. Heckert <aurium@gmail.com>
freedom through controlcan dominate our thinking
c
GNU logo by Aurelio A. Heckert <aurium@gmail.com>
2.the future of scholarly publishing - and
how to stop it
(with attribution to zittrain)
information access allows us to exploit technologies and change the processes
of scientific innovation
information flow drives the processes by which we manage complexity in science
network-driven process revolutions
computers + technology standards = Internet
network-driven process revolutions
computers + technology standards = Internet
documents + technology standards = World Wide Web
network-driven process revolutions
computers + technology standards = Internet
documents + technology standards = World Wide Web
knowledge + legal standards = Research Web
network-driven process revolutions
This is a research tool.
IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
“papers”
IGFBP-5 plays a role in the regulation of cellular senescence via a p53-dependent pathway and in aging-associated vascular diseases
“networked knowledge”
ideas
ideas
exponential content growth
0
1.25
2.50
3.75
5.00
1990 1994 1998 2002
our brain capacity
incremental innovation:ears are good!
incremental innovation:big ears are better!
keyword search
keywords + relevance from links
(non incremental innovation)
abstracts only...
http://orpheus-1.ucsd.edu/acq/license/cdlelsevier2004.pdf
indexing: disallowed.
(no) right of way
image from the public library of sciencelicensed to the public under CC-BY 3.0
>500 journals under CC-BY
c
PubMedCentral ~ 1,000,000 articlespermissions granted: 50,000
(6% of PMC legal for transformative use)(.003 of all PubMed records)
are we going to “watch” literature like TV, or do something with it?
3.open access databases
3.open access databases
(it can make OA to literature look easy)
databases as unique entities, instead of nodes in a network
NeuronDBBAMS
Literature
Homologene
SWAN
Entrez Gene
Gene Ontology
Mammalian Phenotype
PDSPki
BrainPharm
AlzGene
Antibodies
PubChem
MESH
Reactome
Allen Brain Atlas
credit: W3C HCLS
prefix go: <http://purl.org/obo/owl/GO#>prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#>
prefix owl: <http://www.w3.org/2002/07/owl#>prefix mesh: <http://purl.org/commons/record/mesh/>
prefix sc: <http://purl.org/science/owl/sciencecommons/>prefix ro: <http://www.obofoundry.org/ro/ro.owl#>
select ?genename ?processnamewhere
{ graph <http://purl.org/commons/hcls/pubmesh> { ?paper ?p mesh:D017966 .
?article sc:identified_by_pmid ?paper. ?gene sc:describes_gene_or_gene_product_mentioned_by ?article.
} graph <http://purl.org/commons/hcls/goa>
{ ?protein rdfs:subClassOf ?res. ?res owl:onProperty ro:has_function.
?res owl:someValuesFrom ?res2. ?res2 owl:onProperty ro:realized_as.
?res2 owl:someValuesFrom ?process. graph <http://purl.org/commons/hcls/20070416/classrelations>
{{?process <http://purl.org/obo/owl/obo#part_of> go:GO_0007166} union
{?process rdfs:subClassOf go:GO_0007166 }} ?protein rdfs:subClassOf ?parent.
?parent owl:equivalentClass ?res3. ?res3 owl:hasValue ?gene.
} graph <http://purl.org/commons/hcls/gene>
{ ?gene rdfs:label ?genename } graph <http://purl.org/commons/hcls/20070416>
{ ?process rdfs:label ?processname}}
Mesh: Pyramidal Neurons
Pubmed: Journal Articles
Entrez Gene: Genes
GO: Signal Transduction
better answers through better formats:
DRD1, 1812 adenylate cyclase activationADRB2, 154 adenylate cyclase activationADRB2, 154 arrestin mediated desensitization of G-protein coupled receptor protein signaling pathwayDRD1IP, 50632 dopamine receptor signaling pathwayDRD1, 1812 dopamine receptor, adenylate cyclase activating pathwayDRD2, 1813 dopamine receptor, adenylate cyclase inhibiting pathwayGRM7, 2917 G-protein coupled receptor protein signaling pathwayGNG3, 2785 G-protein coupled receptor protein signaling pathwayGNG12, 55970 G-protein coupled receptor protein signaling pathwayDRD2, 1813 G-protein coupled receptor protein signaling pathwayADRB2, 154 G-protein coupled receptor protein signaling pathwayCALM3, 808 G-protein coupled receptor protein signaling pathwayHTR2A, 3356 G-protein coupled receptor protein signaling pathwayDRD1, 1812 G-protein signaling, coupled to cyclic nucleotide second messengerSSTR5, 6755 G-protein signaling, coupled to cyclic nucleotide second messengerMTNR1A, 4543 G-protein signaling, coupled to cyclic nucleotide second messengerCNR2, 1269 G-protein signaling, coupled to cyclic nucleotide second messengerHTR6, 3362 G-protein signaling, coupled to cyclic nucleotide second messengerGRIK2, 2898 glutamate signaling pathwayGRIN1, 2902 glutamate signaling pathwayGRIN2A, 2903 glutamate signaling pathwayGRIN2B, 2904 glutamate signaling pathwayADAM10, 102 integrin-mediated signaling pathwayGRM7, 2917 negative regulation of adenylate cyclase activityLRP1, 4035 negative regulation of Wnt receptor signaling pathwayADAM10, 102 Notch receptor processingASCL1, 429 Notch signaling pathwayHTR2A, 3356 serotonin receptor signaling pathwayADRB2, 154 transmembrane receptor protein tyrosine kinase activation (dimerization)PTPRG, 5793 transmembrane receptor protein tyrosine kinase signaling pathwayEPHA4, 2043 transmembrane receptor protein tyrosine kinase signaling pathwayNRTN, 4902 transmembrane receptor protein tyrosine kinase signaling pathwayCTNND1, 1500 Wnt receptor signaling pathway`
DRD1, 1812 adenylate cyclase activationADRB2, 154 adenylate cyclase activationADRB2, 154 arrestin mediated desensitization of G-protein coupled receptor protein signaling pathwayDRD1IP, 50632 dopamine receptor signaling pathwayDRD1, 1812 dopamine receptor, adenylate cyclase activating pathwayDRD2, 1813 dopamine receptor, adenylate cyclase inhibiting pathwayGRM7, 2917 G-protein coupled receptor protein signaling pathwayGNG3, 2785 G-protein coupled receptor protein signaling pathwayGNG12, 55970 G-protein coupled receptor protein signaling pathwayDRD2, 1813 G-protein coupled receptor protein signaling pathwayADRB2, 154 G-protein coupled receptor protein signaling pathwayCALM3, 808 G-protein coupled receptor protein signaling pathwayHTR2A, 3356 G-protein coupled receptor protein signaling pathwayDRD1, 1812 G-protein signaling, coupled to cyclic nucleotide second messengerSSTR5, 6755 G-protein signaling, coupled to cyclic nucleotide second messengerMTNR1A, 4543 G-protein signaling, coupled to cyclic nucleotide second messengerCNR2, 1269 G-protein signaling, coupled to cyclic nucleotide second messengerHTR6, 3362 G-protein signaling, coupled to cyclic nucleotide second messengerGRIK2, 2898 glutamate signaling pathwayGRIN1, 2902 glutamate signaling pathwayGRIN2A, 2903 glutamate signaling pathwayGRIN2B, 2904 glutamate signaling pathwayADAM10, 102 integrin-mediated signaling pathwayGRM7, 2917 negative regulation of adenylate cyclase activityLRP1, 4035 negative regulation of Wnt receptor signaling pathwayADAM10, 102 Notch receptor processingASCL1, 429 Notch signaling pathwayHTR2A, 3356 serotonin receptor signaling pathwayADRB2, 154 transmembrane receptor protein tyrosine kinase activation (dimerization)PTPRG, 5793 transmembrane receptor protein tyrosine kinase signaling pathwayEPHA4, 2043 transmembrane receptor protein tyrosine kinase signaling pathwayNRTN, 4902 transmembrane receptor protein tyrosine kinase signaling pathwayCTNND1, 1500 Wnt receptor signaling pathway`
this query is probably prohibited in the presence of copyleft / non commercial licensing on the underlying databases
when “freedom” isn’t free:
what do these ideas mean in
a world of integrated data?
license propagation: whatsoever you do to the least of the databases, you do to the integrated knowledgebase
license propagation: whatsoever you do to the least of the databases, you do to the integrated knowledgebase
(the most restrictive license wins)
http://nar.oxfordjournals.org/cgi/content/full/gkm1037/DC1/1
resolving 1000 licenses: impossible.
inspiration for innovation: the human genome
inspiration for innovation: the human genome
the public domainis the foundation.
not the license.
daily global information aggregation is legally secure
the freedom to integrate
the public domain: allows all of us to participate in making “too much data” a Good Thing
licensing: adds “too many contracts” to “too much data”
how do we get legal interoperability among databases?
protocol for open access to databases
“The motivation behind this memorandum is interoperability of scientific data.”
promote legal predictability and certainty.
be easy to use and understand.
impose the lowest possible transaction costs on users.
our conclusions after 18 months of research(and lots of lawyers)
is it legal?
+
+
+
+ +
+
++ +
is it legal?
There are no mechanisms to manage transfer or negotiations of rights unrelated to integration (for example, patent rights over uses of the data).
1 Converge on the public domain by waiving all rights based on intellectual property
2 Converge on the public domain by waiving other statutory or intellectual property rights.
3 Converge on the public domain by imposing no contractual controls.
4 Provide for interoperation with databases not available under the Protocol through open metadata
http://visibleearth.nasa.gov/
a protocol, not a license.
conflicts with the protection instinct
conflicts with the protection instinct
the protection instinct is frequently an instinct to protect “freedom”
and after we release the legal controls, we run into the hard stuff.
and after we release the legal controls, we run into the hard stuff.
(doing this technically isn’t simple)
and after we release the legal controls, we run into the hard stuff.
(doing this technically isn’t simple)
(and it probably requires libraries to work in the long term)
open access coffee ontology
ontologies
taxonomies
triple stores
RDF
OWL
annotation
legal access
enhanced publishing
preservation
citations
provenance
new browsers
free as in speech
free as in speech
free as in beer
free as in a puppy
free as in speech
free as in beer
free as in a puppy
free as in speech
free as in beer
Average Cost Of 100 Pound Dog Over A Year
Good Quality Dog Food$70 x 12 = $840Dog Accessories (collar, leash, etc.)$30Dog Toys$30 - $50Vaccines$35Flea, Tick, & Heartworm Prevention$320Dog Treats$200Boarding$100 - $200 (at $15 - $20 a day)Emergency Costs$0 - $2500 or moreTotal$1375 or much more
call to action
1. copyrights matter. retain enough rights to enable new technologies
2. data matters.ask authors to make data available under OA terms.
3. invest in the preservation and annotation of the public domain.OA doesn’t stop when you post.
thank you
wilbanks@creativecommons.org
http://sciencecommons.org